Legacy API Docs. These docs are for Virtool 4.3.3.

HMMs

Find

Find HMM annotations.

The response data also includes information about the installation state of the HMM collection. The installed field describes the installed HMM release. The release field describes the latest available release from the linked GitHub repository.

GET

/api/hmms

Parameters

Name	Type	Default	Description
find	string		term to search by
page	integer	1	page number of results to return
per_page	integer	15	number of documents to return per page

Example

GET /api/hmms?per_page=2

Response

Status: 200 OK

{
  "documents": [
    {
      "names": ["P3 protein", "coat protein", "P1 protein"],
      "families": {
        "Asfarviridae": 1,
        "Potyviridae": 179
      },
      "cluster": 1,
      "count": 185,
      "id": "7sisu7e2"
    },
    {
      "names": [
        "replication-associated protein",
        "replication associated protein",
        "Rep"
      ],
      "families": {
        "Geminiviridae": 235,
        "None": 2
      },
      "cluster": 2,
      "count": 253,
      "id": "ladu789k"
    }
  ],
  "total_count": 5585,
  "found_count": 5585,
  "page_count": 2793,
  "per_page": 2,
  "page": 1,
  "status": {
    "installed": {
      "id": 8460302,
      "name": "v0.2.0",
      "body": "- the first release using TravisCI for building and testing\r\n- merge annotations and profiles into one archive",
      "filename": "vthmm.tar.gz",
      "size": 86059385,
      "html_url": "https://github.com/virtool/virtool-hmm/releases/tag/v0.2.0",
      "published_at": "2017-11-10T00:27:20Z",
      "ready": true,
      "user": {
        "id": "igboyes"
      }
    },
    "process": {
      "id": "bzfk2t76"
    },
    "release": {
      "id": 8472569,
      "name": "v0.2.1",
      "body": "- remove some annotations that didn't have corresponding profiles",
      "etag": "W/\"81fc9c9b3e02ff03c8cc1163e8031ee3\"",
      "filename": "vthmm.tar.gz",
      "size": 85904451,
      "html_url": "https://github.com/virtool/virtool-hmm/releases/tag/v0.2.1",
      "download_url": "https://github.com/virtool/virtool-hmm/releases/download/v0.2.1/vthmm.tar.gz",
      "published_at": "2017-11-10T19:12:43Z",
      "content_type": "application/gzip",
      "newer": true
    },
    "id": "hmm",
    "updating": false
  }
}

Get

Get the complete representation of a single HMM annotation.

GET

/api/hmms/:id

Example

GET /api/hmms/zltnktou

Response

Status: 200 OK

{
  "families": {
    "None": 1,
    "Geminiviridae": 203
  },
  "total_entropy": 72.08,
  "length": 136,
  "cluster": 3,
  "entries": [
    {
      "accession": "NP_040323.1",
      "gi": "9626084",
      "organism": "Pepper huasteco yellow vein virus",
      "name": "AL2 protein"
    },
    {
      "accession": "NP_044924.1",
      "gi": "9629639",
      "organism": "Tomato mottle Taino virus",
      "name": "transactivator protein"
    }
  ],
  "genera": {
    "Begomovirus": 197,
    "Topocuvirus": 1,
    "None": 2,
    "Curtovirus": 4
  },
  "mean_entropy": 0.53,
  "count": 216,
  "names": ["AC2 protein", "C2 protein", "AC2"],
  "hidden": false,
  "id": "zltnktou"
}

Errors

Status	Message	Reason
404	Not found	HMM annotation does not exist

Get Status

Get the status information for the HMM collection.

The HMM status describes the latest available release of the Virtool HMM data and the currently installed release.

When the release.newer is true the release can be used to update the HMM install installation.

When updating is true there is already an update proces in progress.

The process.id describes the process document that describes the HMM installation process.

GET

/api/hmms/status

Example

GET /api/hmms/status

Response

Status: 200 OK

{
  "installed": {
    "id": 8460302,
    "name": "v0.2.0",
    "body": "- the first release using TravisCI for building and testing\r\n- merge annotations and profiles into one archive",
    "filename": "vthmm.tar.gz",
    "size": 86059385,
    "html_url": "https://github.com/virtool/virtool-hmm/releases/tag/v0.2.0",
    "published_at": "2017-11-10T00:27:20Z",
    "ready": true,
    "user": {
      "id": "igboyes"
    }
  },
  "process": {
    "id": "bzfk2t76"
  },
  "release": {
    "id": 8472569,
    "name": "v0.2.1",
    "body": "- remove some annotations that didn't have corresponding profiles",
    "etag": "W/\"81fc9c9b3e02ff03c8cc1163e8031ee3\"",
    "filename": "vthmm.tar.gz",
    "size": 85904451,
    "html_url": "https://github.com/virtool/virtool-hmm/releases/tag/v0.2.1",
    "download_url": "https://github.com/virtool/virtool-hmm/releases/download/v0.2.1/vthmm.tar.gz",
    "published_at": "2017-11-10T19:12:43Z",
    "content_type": "application/gzip",
    "newer": true
  },
  "id": "hmm",
  "updating": false
}

Get Release

Check GitHub for the latest release of the Virtool HMM data set.

This is the only method for updating the available release information. When the newer is true the release can be used to update the HMM install installation.

GET

/api/hmms/status/release

Example

GET /api/hmms/status/release

Response

Status: 200 OK

{
  "id": 8472569,
  "name": "v0.2.1",
  "body": "- remove some annotations that didn't have corresponding profiles",
  "etag": "W/\"81fc9c9b3e02ff03c8cc1163e8031ee3\"",
  "filename": "vthmm.tar.gz",
  "size": 85904451,
  "html_url": "https://github.com/virtool/virtool-hmm/releases/tag/v0.2.1",
  "download_url": "https://github.com/virtool/virtool-hmm/releases/download/v0.2.1/vthmm.tar.gz",
  "published_at": "2017-11-10T19:12:43Z",
  "content_type": "application/gzip",
  "newer": true
}

Errors

Status	Message	Reason
502	Repository does not exist	the GitHub repository set in the `hmm_slug` setting does not exist
502	Could not reach GitHub	the server could not connect to GitHub

List Updates

List the update history for the.

Most recently applied updates are first in returned the array. Updates that are in the process of being installed are included in the response. The ready field is true when the update has been successfully installed.

GET

/api/hmms/status/updates

Example

GET /api/hmms/status/updates

Response

Status: 200 OK

[
  {
    "id": 8460302,
    "name": "v0.2.0",
    "body": "- the first release using TravisCI for building and testing\r\n- merge annotations and profiles into one archive",
    "filename": "vthmm.tar.gz",
    "size": 86059385,
    "html_url": "https://github.com/virtool/virtool-hmm/releases/tag/v0.2.0",
    "published_at": "2017-11-10T00:27:20Z",
    "ready": true,
    "user": {
      "id": "igboyes"
    }
  }
]

Install

Requires modify_hmm permission

Install the locally cached release as the official virus HMM reference.

Installing when a previous release has already been installed will remove all HMMs not referenced in existing analyses and install the new release.

POST

/api/hmms/status/updates

Example

POST /api/hmms/updates

Response

Status: 201 Created

{
  "id": 8460302,
  "name": "v0.2.0",
  "body": "- the first release using TravisCI for building and testing\r\n- merge annotations and profiles into one archive",
  "filename": "vthmm.tar.gz",
  "size": 86059385,
  "html_url": "https://github.com/virtool/virtool-hmm/releases/tag/v0.2.0",
  "published_at": "2017-11-10T00:27:20Z",
  "created_at": "2018-06-15T18:26:30.787000Z",
  "ready": false,
  "user": {
    "id": "igboyes"
  }
}

Errors

Status	Message	Reason
400	Target release does not exist	no release information has been fetched and cached from GitHub
403	Not permitted	user does not have `modify_hmm` permission

Purge

Permanently remove all HMMs that are not referenced by NuVs analysis records.

HMMs that are referenced in NuVs analysis records will be soft-deleted. They will not be returned in search results, but the data is still available for constructing annotated NuVs results.

DELETE

/api/hmms

Example

DELETE /api/hmms

Response

Status: 204 No content

Errors

Status	Message	Reason
403	Not permitted	user does not have `modify_hmm` permission